Multiple Sequence Alignment (MSA) Viewer — Online & Colored
Align several DNA or protein sequences and view a colored alignment with a consensus.
🔒 Local processing — pasted sequences are not uploaded
Paste several sequences in FASTA and get a multiple sequence alignment you can actually read. The viewer aligns them with a center-star method over the pairwise aligner, colors each residue, and shows a consensus row shaded by conservation — so conserved blocks and variable positions stand out at a glance. Export the alignment as a publication-ready SVG or PNG figure, download it as FASTA, or copy a link that reproduces it for a colleague.
0 sequence(s)
Provide at least two sequences.
Alignment uses the center-star heuristic over the pairwise global aligner — well suited to a handful of homologous sequences. The consensus row is shaded by per-column conservation. Export the figure as SVG/PNG, download the alignment as FASTA, or copy a share link that reproduces it.
How to use the MSA Viewer tool
- 1Paste two or more sequences in FASTA format (or load the example).
- 2Read the colored alignment, consensus and conservation; DNA and protein are colored automatically.
- 3Export the figure as SVG/PNG, download the alignment as FASTA, or share the link.
Frequently asked questions
- How does the alignment work?
- It uses the center-star heuristic: every sequence is aligned to the most central sequence with the pairwise global aligner, and those alignments are merged into one MSA. It's well suited to a handful of homologous sequences; for large datasets use a dedicated tool like MAFFT or MUSCLE.
- Can I align protein sequences too?
- Yes. The viewer detects whether your sequences are nucleotide or protein and colors them accordingly (nucleotide palette, or a Clustal-style amino-acid grouping).
- Can I export the alignment figure?
- Yes — export the colored alignment as a vector SVG or a high-resolution PNG for figures and slides, or download the aligned sequences as FASTA.